Core

momapy.celldesigner.core

Classes for CellDesigner maps

Classes:

Name	Description
AndGate	Class for and gates
AndGateLayout	Class for and gate layouts
AntisenseRNA	Class for antisense RNAs
AntisenseRNALayout	Class for antisense RNA layouts
AntisenseRNATemplate	Class for antisense RNA templates
BooleanLogicGate	Base class for Boolean logic gates
Catalysis	Class for catalyses
CatalysisLayout	Class for catalysis layouts
Catalyzer	Class for catalyzers
CellDesignerDoubleHeadedArc	Base class for CellDesigner double-headed arcs
CellDesignerLayout	Class for CellDesigner layouts
CellDesignerMap	Class for CellDesigner maps
CellDesignerModel	Class for CellDesigner models
CellDesignerModelElement	Base class for CellDesigner model elements
CellDesignerNode	Base class for CellDesigner nodes
CellDesignerSingleHeadedArc	Base class for CellDesigner single-headed arcs
CodingRegion	Class for coding regions
Compartment	Class for compartments
Complex	Class for complexes
ComplexLayout	Class for complex layouts
ConsumptionLayout	Class for consumption layouts
Degraded	Class for degradeds
DegradedLayout	Class for degraded layouts
Dissociation	Class for dissociations
DissociationLayout	Class for dissociation layouts
Drug	Class for drugs
DrugLayout	Class for drug layouts
Gene	Class for genes
GeneLayout	Class for gene layouts
GeneTemplate	Class for gene templates
GenericProtein	Class for generic proteins
GenericProteinLayout	Class for generic protein layouts
GenericProteinTemplate	Class for generic protein templates
HeterodimerAssociation	Class for heterodimer associations
HeterodimerAssociationLayout	Class for heterodimer association layouts
Inhibition	Class for inhibitions
InhibitionLayout	Class for inhibition layouts
Inhibitor	Class for inhibitors
Ion	Class for ions
IonChannel	Class for ion channels
IonChannelLayout	Class for generic ion channel layouts
IonChannelTemplate	Class for ion channel templates
IonLayout	Class for ion layouts
KnownOrUnknownModulator	Base class for know or unknown modulators
KnownTransitionOmitted	Class for known transitions omitted
KnownTransitionOmittedLayout	Class for known transition omitted layouts
LogicArcLayout	Class for logic arc layouts
Modification	Class for modifications
ModificationLayout	Class for modification layouts
ModificationResidue	Class for modification residues
ModificationSite	Class for modification sites
ModificationState	Class for modification states
Modulation	Class for modulations
ModulationLayout	Class for modulation layouts
Modulator	Class for modulators
NegativeInfluence	Class for negative influences
NotGate	Class for not gates
NotGateLayout	Class for not gate layouts
OrGate	Class for or gates
OrGateLayout	Class for or gate layouts
OvalCompartmentLayout	Class for oval compartment layouts
Phenotype	Class for phenotypes
PhenotypeLayout	Class for phenotype layouts
PhysicalStimulation	Class for physical stimulations
PhysicalStimulationLayout	Class for physical stimulation layouts
PhysicalStimulator	Class for physical stimulators
PositiveInfluence	Class for positive influences
PositiveInfluenceLayout	Class for positive influence layouts
Product	Class for products
ProductionLayout	Class for production layouts
Protein	Base class for proteins
ProteinBindingDomain	Class for protein binding domains
ProteinTemplate	Base class for protein templates
RNA	Class for RNAs
RNALayout	Class for RNA layouts
RNATemplate	Class for RNA templates
Reactant	Class for reactants
Reaction	Base class for reactions
Receptor	Class for receptors
ReceptorLayout	Class for receptor layouts
ReceptorTemplate	Class for receptor templates
RectangleCompartmentLayout	Class for rectangle compartment layouts
Region	Class for regions
RegulatoryRegion	Class for regulatory regions
SimpleMolecule	Class for simple molecules
SimpleMoleculeLayout	Class for simple chemical layouts
Species	Base class for species
SpeciesTemplate	Base class for species templates
StateTransition	Class for state transitions
StateTransitionLayout	Class for state transition layouts
StructuralState	Class for structural states
StructuralStateLayout	Class for structural states layouts
Transcription	Class for transcriptions
TranscriptionLayout	Class for transcription layouts
TranscriptionStartingSiteL	Class for left transcription starting sites
TranscriptionStartingSiteR	Class for right transcription starting sites
Translation	Class for translation
TranslationLayout	Class for translation layouts
Transport	Class for transports
TransportLayout	Class for transport layouts
Trigger	Class for triggers
Triggering	Class for triggerings
TriggeringLayout	Class for triggering layouts
TruncatedProtein	Class for truncated proteins
TruncatedProteinLayout	Class for truncated protein layouts
TruncatedProteinTemplate	Class for truncated protein templates
Truncation	Class for truncations
TruncationLayout	Class for truncation layouts
Unknown	Class for unknown species
UnknownCatalysis	Class for unknown catalyses
UnknownCatalysisLayout	Class for unknown catalysis layouts
UnknownCatalyzer	Class for unknown catalyzers
UnknownGate	Class for unknown gates
UnknownGateLayout	Class for unknown gate layouts
UnknownInhibition	Class for unknown inhibitions
UnknownInhibitionLayout	Class for unknown inhibition layouts
UnknownInhibitor	Class for unknown inhibitors
UnknownLayout	Class for unknown species layouts
UnknownModulation	Class for unknown modulations
UnknownModulationLayout	Class for unknown modulation layouts
UnknownModulator	Class for unknown modulators
UnknownNegativeInfluence	Class for unknown negative influences
UnknownPhysicalStimulation	Class for unknown physical stimulations
UnknownPhysicalStimulationLayout	Class for unknown physical stimulation layouts
UnknownPositiveInfluence	Class for unknown positive influences
UnknownPositiveInfluenceLayout	Class for unknown positive influence layouts
UnknownTransition	Class for unknown transitions
UnknownTransitionLayout	Class for unknown transition layouts
UnknownTriggering	Class for unknown triggerings
UnknownTriggeringLayout	Class for unknown triggering layouts

AndGate dataclass

AndGate(*, id_: str = make_uuid4_as_str(), inputs: frozenset[Species] = frozenset())

Bases: BooleanLogicGate

Class for and gates

AndGateLayout dataclass

AndGateLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 15.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 15.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: _SimpleNodeMixin, _TextMixin, CellDesignerNode

Class for and gate layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

AntisenseRNA dataclass

AntisenseRNA(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: AntisenseRNATemplate, modifications: frozenset[Modification] = frozenset())

Bases: Species

Class for antisense RNAs

AntisenseRNALayout dataclass

AntisenseRNALayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, angle: float = 45.0)

Bases: _MultiNodeMixin, CellDesignerNode

Class for antisense RNA layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
angle	float	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = 45.0

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/celldesigner/core.py

def east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint3() / 2 + shape.joint2() / 2

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/celldesigner/core.py

def east_north_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint3() * 0.25 + shape.joint2() * 0.75

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/celldesigner/core.py

def east_south_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint3() * 0.75 + shape.joint2() * 0.25

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/celldesigner/core.py

def north(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1() / 2 + shape.joint2() / 2

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint2()

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_north_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1() * 0.25 + shape.joint2() * 0.75

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_north_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1() * 0.75 + shape.joint2() * 0.25

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1()

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/celldesigner/core.py

def south(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() / 2 + shape.joint3() / 2

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint3()

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_south_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() * 0.25 + shape.joint3() * 0.75

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_south_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() * 0.75 + shape.joint3() * 0.25

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4()

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/celldesigner/core.py

def west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() / 2 + shape.joint1() / 2

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/celldesigner/core.py

def west_north_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() * 0.25 + shape.joint1() * 0.75

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/celldesigner/core.py

def west_south_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() * 0.75 + shape.joint1() * 0.25

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

AntisenseRNATemplate dataclass

AntisenseRNATemplate(*, id_: str = make_uuid4_as_str(), name: str, regions: frozenset[ModificationSite | CodingRegion | ProteinBindingDomain] = frozenset())

Bases: SpeciesTemplate

Class for antisense RNA templates

BooleanLogicGate dataclass

BooleanLogicGate(*, id_: str = make_uuid4_as_str(), inputs: frozenset[Species] = frozenset())

Bases: CellDesignerModelElement

Base class for Boolean logic gates

Catalysis dataclass

Catalysis(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: Modulation

Class for catalyses

CatalysisLayout dataclass

CatalysisLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 7.0, arrowhead_width: float = 7.0)

Bases: CellDesignerSingleHeadedArc

Class for catalysis layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

Catalyzer dataclass

Catalyzer(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)

Bases: PhysicalStimulator

Class for catalyzers

CellDesignerDoubleHeadedArc dataclass

CellDesignerDoubleHeadedArc(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = None, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = None, end_arrowhead_stroke_dasharray: tuple[float, ...] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = None, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = None, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = None, start_arrowhead_stroke_dasharray: tuple[float, ...] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = None, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: DoubleHeadedArc

Base class for CellDesigner double-headed arcs

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_arrowhead_base	Return the base anchor point of the double-headed arc end arrowhead
end_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
end_arrowhead_length	Return the length of the double-headed arc end arrowhead
end_arrowhead_tip	Return the tip anchor point of the double-headed arc end arrowhead
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the double-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base	Return the base anchor point of the double-headed arc start arrowhead
start_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
start_arrowhead_drawing_elements	Return the drawing elements of the double-headed arc start arrowhead
start_arrowhead_length	Return the length of the double-headed arc start arrowhead
start_arrowhead_tip	Return the tip anchor point of the double-headed arc start arrowhead
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_arrowhead_base

end_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc end arrowhead"""
    arrowhead_length = self.end_arrowhead_length()
    if arrowhead_length == 0:
        return self.end_point()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.end_arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

end_arrowhead_bbox

end_arrowhead_bbox()

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def end_arrowhead_bbox(self):
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.end_arrowhead_drawing_elements()
    )

end_arrowhead_border

end_arrowhead_border(point)

Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def end_arrowhead_border(self, point):
    """Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.end_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.end_arrowhead_tip()
    return point

end_arrowhead_length

end_arrowhead_length() -> float

Return the length of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc end arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._end_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

end_arrowhead_tip

end_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc end arrowhead"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the double-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the double-headed arc path"""
    start_arrowhead_length = self.start_arrowhead_length()
    end_arrowhead_length = self.end_arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten + start_arrowhead_length, "start")
            .shortened(self.end_shorten + end_arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten + start_arrowhead_length, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + end_arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerDoubleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_arrowhead_base

start_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc start arrowhead"""
    arrowhead_length = self.start_arrowhead_length()
    if arrowhead_length == 0:
        return self.start_point()
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return self.start_arrowhead_tip() + (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.start_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

start_arrowhead_bbox

start_arrowhead_bbox() -> Bbox

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.start_arrowhead_drawing_elements()
    )

start_arrowhead_border

start_arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def start_arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    point = momapy.drawing.get_drawing_elements_border(
        self.start_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.start_arrowhead_tip()
    return point

start_arrowhead_drawing_elements

start_arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the double-headed arc start arrowhead"""
    drawing_elements = self._start_arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_start_arrowhead",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_start_arrowhead",
        fill=self.start_arrowhead_fill,
        filter=self.start_arrowhead_filter,
        stroke=self.start_arrowhead_stroke,
        stroke_dasharray=self.start_arrowhead_stroke_dasharray,
        stroke_dashoffset=self.start_arrowhead_stroke_dashoffset,
        stroke_width=self.start_arrowhead_stroke_width,
        transform=self.start_arrowhead_transform,
    )
    transformation = self._get_start_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

start_arrowhead_length

start_arrowhead_length() -> float

Return the length of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc start arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._start_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return abs(bbox.west().x)

start_arrowhead_tip

start_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc start arrowhead"""
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.start_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

CellDesignerLayout dataclass

CellDesignerLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, fill: NoneValueType | Color | None = NoneValue, filter: NoneValueType | Filter | None = None, height: float, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float)

Bases: Layout

Class for CellDesigner layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
is_sublayout	Return true if another given layout is a sublayout of the layout, false otherwise
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

is_sublayout

is_sublayout(other, flattened=False, unordered=False)

Return true if another given layout is a sublayout of the layout, false otherwise

Source code in src/momapy/core.py

def is_sublayout(self, other, flattened=False, unordered=False):
    """Return `true` if another given layout is a sublayout of the layout, `false` otherwise"""

    def _is_sublist(list1, list2, unordered=False) -> bool:
        if not unordered:
            i = 0
            for elem1 in list1:
                elem2 = list2[i]
                while elem2 != elem1 and i < len(list2) - 1:
                    i += 1
                    elem2 = list2[i]
                if not elem2 == elem1:
                    return False
                i += 1
        else:
            dlist1 = collections.defaultdict(int)
            dlist2 = collections.defaultdict(int)
            for elem1 in list1:
                dlist1[elem1] += 1
            for elem2 in list2:
                dlist2[elem2] += 1
            for elem in dlist1:
                if dlist1[elem] > dlist2[elem]:
                    return False
        return True

    if self.childless() != other.childless():
        return False
    if flattened:
        return _is_sublist(
            self.flattened()[1:],
            other.flattened()[1:],
            unordered=unordered,
        )
    return _is_sublist(self.children(), other.children(), unordered=unordered)

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

CellDesignerMap dataclass

CellDesignerMap(*, id_: str = make_uuid4_as_str(), model: CellDesignerModel | None = None, layout: CellDesignerLayout | None = None, layout_model_mapping: LayoutModelMapping | None = None)

Bases: Map

Class for CellDesigner maps

Methods:

Name	Description
get_mapping	Return the layout elements mapped to the given model element
is_submap	Return true if another given map is a submap of the Map, false otherwise

get_mapping

get_mapping(map_element: MapElement | tuple[ModelElement, ModelElement])

Return the layout elements mapped to the given model element

Source code in src/momapy/core.py

def get_mapping(
    self,
    map_element: MapElement | tuple[ModelElement, ModelElement],
):
    """Return the layout elements mapped to the given model element"""
    return self.layout_model_mapping.get_mapping(map_element)

is_submap

is_submap(other)

Return true if another given map is a submap of the Map, false otherwise

Source code in src/momapy/core.py

def is_submap(self, other):
    """Return `true` if another given map is a submap of the `Map`, `false` otherwise"""
    if (
        self.model is None
        or self.layout is None
        or self.layout_model_mapping is None
    ):
        return False
    return (
        self.model.is_submodel(other.model)
        and self.layout.is_sublayout(other.layout)
        and self.layout_model_mapping.is_submapping(other.layout_model_mapping)
    )

CellDesignerModel dataclass

CellDesignerModel(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartments: frozenset[Compartment] = frozenset(), species: frozenset[Species] = frozenset(), reactions: frozenset[Reaction] = frozenset(), species_templates: frozenset[SpeciesTemplate] = frozenset(), boolean_logic_gates: frozenset[BooleanLogicGate] = frozenset(), modulations: frozenset[Modulation | UnknownModulation] = frozenset())

Bases: Model

Class for CellDesigner models

CellDesignerModelElement dataclass

CellDesignerModelElement(*, id_: str = make_uuid4_as_str())

Bases: ModelElement

Base class for CellDesigner model elements

CellDesignerNode dataclass

CellDesignerNode(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float)

Bases: SBGNNode

Base class for CellDesigner nodes

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

CellDesignerSingleHeadedArc dataclass

CellDesignerSingleHeadedArc(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = None, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: SingleHeadedArc

Base class for CellDesigner single-headed arcs

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

CodingRegion dataclass

CodingRegion(*, id_: str = make_uuid4_as_str(), name: str | None = None, active: bool = False)

Bases: Region

Class for coding regions

Compartment dataclass

Compartment(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, outside: Optional[ForwardRef(Compartment, module=core)] = None)

Bases: Compartment, CellDesignerModelElement

Class for compartments

Complex dataclass

Complex(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, structural_states: frozenset[StructuralState] = frozenset(), subunits: frozenset[Species] = frozenset())

Bases: Species

Class for complexes

ComplexLayout dataclass

ComplexLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, cut_corners: float = 6.0)

Bases: _MultiNodeMixin, CellDesignerNode

Class for complex layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

ConsumptionLayout dataclass

ConsumptionLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = None, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: CellDesignerSingleHeadedArc

Class for consumption layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

Degraded dataclass

Degraded(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1)

Bases: Species

Class for degradeds

DegradedLayout dataclass

DegradedLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 30.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1)

Bases: _MultiNodeMixin, CellDesignerNode

Class for degraded layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Dissociation dataclass

Dissociation(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())

Bases: Reaction

Class for dissociations

DissociationLayout dataclass

DissociationLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = white, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 10.0, end_arrowhead_sep: float = 2.0, end_arrowhead_width: float = 10.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)

Bases: ReactionLayout, _ReactionNodeMixin

Class for dissociation layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_arrowhead_base	Return the base anchor point of the double-headed arc end arrowhead
end_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
end_arrowhead_length	Return the length of the double-headed arc end arrowhead
end_arrowhead_tip	Return the tip anchor point of the double-headed arc end arrowhead
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the double-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base	Return the base anchor point of the double-headed arc start arrowhead
start_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
start_arrowhead_drawing_elements	Return the drawing elements of the double-headed arc start arrowhead
start_arrowhead_length	Return the length of the double-headed arc start arrowhead
start_arrowhead_tip	Return the tip anchor point of the double-headed arc start arrowhead
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_arrowhead_base

end_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc end arrowhead"""
    arrowhead_length = self.end_arrowhead_length()
    if arrowhead_length == 0:
        return self.end_point()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.end_arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

end_arrowhead_bbox

end_arrowhead_bbox()

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def end_arrowhead_bbox(self):
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.end_arrowhead_drawing_elements()
    )

end_arrowhead_border

end_arrowhead_border(point)

Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def end_arrowhead_border(self, point):
    """Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.end_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.end_arrowhead_tip()
    return point

end_arrowhead_length

end_arrowhead_length() -> float

Return the length of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc end arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._end_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

end_arrowhead_tip

end_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc end arrowhead"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the double-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the double-headed arc path"""
    start_arrowhead_length = self.start_arrowhead_length()
    end_arrowhead_length = self.end_arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten + start_arrowhead_length, "start")
            .shortened(self.end_shorten + end_arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten + start_arrowhead_length, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + end_arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerDoubleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_arrowhead_base

start_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc start arrowhead"""
    arrowhead_length = self.start_arrowhead_length()
    if arrowhead_length == 0:
        return self.start_point()
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return self.start_arrowhead_tip() + (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.start_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

start_arrowhead_bbox

start_arrowhead_bbox() -> Bbox

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.start_arrowhead_drawing_elements()
    )

start_arrowhead_border

start_arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def start_arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    point = momapy.drawing.get_drawing_elements_border(
        self.start_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.start_arrowhead_tip()
    return point

start_arrowhead_drawing_elements

start_arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the double-headed arc start arrowhead"""
    drawing_elements = self._start_arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_start_arrowhead",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_start_arrowhead",
        fill=self.start_arrowhead_fill,
        filter=self.start_arrowhead_filter,
        stroke=self.start_arrowhead_stroke,
        stroke_dasharray=self.start_arrowhead_stroke_dasharray,
        stroke_dashoffset=self.start_arrowhead_stroke_dashoffset,
        stroke_width=self.start_arrowhead_stroke_width,
        transform=self.start_arrowhead_transform,
    )
    transformation = self._get_start_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

start_arrowhead_length

start_arrowhead_length() -> float

Return the length of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc start arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._start_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return abs(bbox.west().x)

start_arrowhead_tip

start_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc start arrowhead"""
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.start_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

Drug dataclass

Drug(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1)

Bases: Species

Class for drugs

DrugLayout dataclass

DrugLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, horizontal_proportion: float = 0.2, sep: float = 4.0)

Bases: _MultiNodeMixin, CellDesignerNode

Class for drug layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Gene dataclass

Gene(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: GeneTemplate, modifications: frozenset[Modification] = frozenset())

Bases: Species

Class for genes

GeneLayout dataclass

GeneLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1)

Bases: _MultiNodeMixin, CellDesignerNode

Class for gene layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

GeneTemplate dataclass

GeneTemplate(*, id_: str = make_uuid4_as_str(), name: str, regions: frozenset[ModificationSite | CodingRegion | RegulatoryRegion | TranscriptionStartingSiteL | TranscriptionStartingSiteR] = frozenset())

Bases: SpeciesTemplate

Class for gene templates

GenericProtein dataclass

GenericProtein(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: GenericProteinTemplate, modifications: frozenset[Modification] = frozenset(), structural_states: frozenset[StructuralState] = frozenset())

Bases: Protein

Class for generic proteins

GenericProteinLayout dataclass

GenericProteinLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, rounded_corners: float = 5.0)

Bases: _MultiNodeMixin, CellDesignerNode

Class for generic protein layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

GenericProteinTemplate dataclass

GenericProteinTemplate(*, id_: str = make_uuid4_as_str(), name: str, modification_residues: frozenset[ModificationResidue] = frozenset())

Bases: ProteinTemplate

Class for generic protein templates

HeterodimerAssociation dataclass

HeterodimerAssociation(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())

Bases: Reaction

Class for heterodimer associations

HeterodimerAssociationLayout dataclass

HeterodimerAssociationLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 8.0, end_arrowhead_width: float = 15.0, start_arrowhead_height: float = 6.0, start_arrowhead_width: float = 6.0)

Bases: ReactionLayout, _ReactionNodeMixin

Class for heterodimer association layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_arrowhead_base	Return the base anchor point of the double-headed arc end arrowhead
end_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
end_arrowhead_length	Return the length of the double-headed arc end arrowhead
end_arrowhead_tip	Return the tip anchor point of the double-headed arc end arrowhead
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the double-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base	Return the base anchor point of the double-headed arc start arrowhead
start_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
start_arrowhead_drawing_elements	Return the drawing elements of the double-headed arc start arrowhead
start_arrowhead_length	Return the length of the double-headed arc start arrowhead
start_arrowhead_tip	Return the tip anchor point of the double-headed arc start arrowhead
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_arrowhead_base

end_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc end arrowhead"""
    arrowhead_length = self.end_arrowhead_length()
    if arrowhead_length == 0:
        return self.end_point()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.end_arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

end_arrowhead_bbox

end_arrowhead_bbox()

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def end_arrowhead_bbox(self):
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.end_arrowhead_drawing_elements()
    )

end_arrowhead_border

end_arrowhead_border(point)

Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def end_arrowhead_border(self, point):
    """Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.end_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.end_arrowhead_tip()
    return point

end_arrowhead_length

end_arrowhead_length() -> float

Return the length of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc end arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._end_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

end_arrowhead_tip

end_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc end arrowhead"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the double-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the double-headed arc path"""
    start_arrowhead_length = self.start_arrowhead_length()
    end_arrowhead_length = self.end_arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten + start_arrowhead_length, "start")
            .shortened(self.end_shorten + end_arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten + start_arrowhead_length, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + end_arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerDoubleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_arrowhead_base

start_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc start arrowhead"""
    arrowhead_length = self.start_arrowhead_length()
    if arrowhead_length == 0:
        return self.start_point()
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return self.start_arrowhead_tip() + (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.start_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

start_arrowhead_bbox

start_arrowhead_bbox() -> Bbox

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.start_arrowhead_drawing_elements()
    )

start_arrowhead_border

start_arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def start_arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    point = momapy.drawing.get_drawing_elements_border(
        self.start_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.start_arrowhead_tip()
    return point

start_arrowhead_drawing_elements

start_arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the double-headed arc start arrowhead"""
    drawing_elements = self._start_arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_start_arrowhead",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_start_arrowhead",
        fill=self.start_arrowhead_fill,
        filter=self.start_arrowhead_filter,
        stroke=self.start_arrowhead_stroke,
        stroke_dasharray=self.start_arrowhead_stroke_dasharray,
        stroke_dashoffset=self.start_arrowhead_stroke_dashoffset,
        stroke_width=self.start_arrowhead_stroke_width,
        transform=self.start_arrowhead_transform,
    )
    transformation = self._get_start_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

start_arrowhead_length

start_arrowhead_length() -> float

Return the length of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc start arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._start_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return abs(bbox.west().x)

start_arrowhead_tip

start_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc start arrowhead"""
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.start_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

Inhibition dataclass

Inhibition(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: Modulation

Class for inhibitions

InhibitionLayout dataclass

InhibitionLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 3.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = None, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0)

Bases: CellDesignerSingleHeadedArc

Class for inhibition layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

Inhibitor dataclass

Inhibitor(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)

Bases: Modulator

Class for inhibitors

Ion dataclass

Ion(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1)

Bases: Species

Class for ions

IonChannel dataclass

IonChannel(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: IonChannelTemplate, modifications: frozenset[Modification] = frozenset(), structural_states: frozenset[StructuralState] = frozenset())

Bases: Protein

Class for ion channels

IonChannelLayout dataclass

IonChannelLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, rounded_corners: float = 5.0, right_rectangle_width: float = 20.0)

Bases: _MultiNodeMixin, CellDesignerNode

Class for generic ion channel layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

IonChannelTemplate dataclass

IonChannelTemplate(*, id_: str = make_uuid4_as_str(), name: str, modification_residues: frozenset[ModificationResidue] = frozenset())

Bases: ProteinTemplate

Class for ion channel templates

IonLayout dataclass

IonLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1)

Bases: _MultiNodeMixin, CellDesignerNode

Class for ion layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

KnownOrUnknownModulator dataclass

KnownOrUnknownModulator(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)

Bases: ModifierSpeciesReference, CellDesignerModelElement

Base class for know or unknown modulators

KnownTransitionOmitted dataclass

KnownTransitionOmitted(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())

Bases: Reaction

Class for known transitions omitted

KnownTransitionOmittedLayout dataclass

KnownTransitionOmittedLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 8.0, end_arrowhead_width: float = 15.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)

Bases: ReactionLayout, _ReactionNodeMixin

Class for known transition omitted layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_arrowhead_base	Return the base anchor point of the double-headed arc end arrowhead
end_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
end_arrowhead_length	Return the length of the double-headed arc end arrowhead
end_arrowhead_tip	Return the tip anchor point of the double-headed arc end arrowhead
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the double-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base	Return the base anchor point of the double-headed arc start arrowhead
start_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
start_arrowhead_drawing_elements	Return the drawing elements of the double-headed arc start arrowhead
start_arrowhead_length	Return the length of the double-headed arc start arrowhead
start_arrowhead_tip	Return the tip anchor point of the double-headed arc start arrowhead
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_arrowhead_base

end_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc end arrowhead"""
    arrowhead_length = self.end_arrowhead_length()
    if arrowhead_length == 0:
        return self.end_point()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.end_arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

end_arrowhead_bbox

end_arrowhead_bbox()

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def end_arrowhead_bbox(self):
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.end_arrowhead_drawing_elements()
    )

end_arrowhead_border

end_arrowhead_border(point)

Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def end_arrowhead_border(self, point):
    """Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.end_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.end_arrowhead_tip()
    return point

end_arrowhead_length

end_arrowhead_length() -> float

Return the length of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc end arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._end_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

end_arrowhead_tip

end_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc end arrowhead"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the double-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the double-headed arc path"""
    start_arrowhead_length = self.start_arrowhead_length()
    end_arrowhead_length = self.end_arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten + start_arrowhead_length, "start")
            .shortened(self.end_shorten + end_arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten + start_arrowhead_length, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + end_arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerDoubleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_arrowhead_base

start_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc start arrowhead"""
    arrowhead_length = self.start_arrowhead_length()
    if arrowhead_length == 0:
        return self.start_point()
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return self.start_arrowhead_tip() + (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.start_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

start_arrowhead_bbox

start_arrowhead_bbox() -> Bbox

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.start_arrowhead_drawing_elements()
    )

start_arrowhead_border

start_arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def start_arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    point = momapy.drawing.get_drawing_elements_border(
        self.start_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.start_arrowhead_tip()
    return point

start_arrowhead_drawing_elements

start_arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the double-headed arc start arrowhead"""
    drawing_elements = self._start_arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_start_arrowhead",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_start_arrowhead",
        fill=self.start_arrowhead_fill,
        filter=self.start_arrowhead_filter,
        stroke=self.start_arrowhead_stroke,
        stroke_dasharray=self.start_arrowhead_stroke_dasharray,
        stroke_dashoffset=self.start_arrowhead_stroke_dashoffset,
        stroke_width=self.start_arrowhead_stroke_width,
        transform=self.start_arrowhead_transform,
    )
    transformation = self._get_start_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

start_arrowhead_length

start_arrowhead_length() -> float

Return the length of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc start arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._start_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return abs(bbox.west().x)

start_arrowhead_tip

start_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc start arrowhead"""
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.start_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

LogicArcLayout dataclass

LogicArcLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = None, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: CellDesignerSingleHeadedArc

Class for logic arc layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

Modification dataclass

Modification(*, id_: str = make_uuid4_as_str(), residue: ModificationResidue | ModificationSite | None = None, state: ModificationState | None = None)

Bases: CellDesignerModelElement

Class for modifications

ModificationLayout dataclass

ModificationLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 16.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 16.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: _SimpleNodeMixin, CellDesignerNode

Class for modification layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

ModificationResidue dataclass

ModificationResidue(*, id_: str = make_uuid4_as_str(), name: str | None = None, order: int | None = None)

Bases: CellDesignerModelElement

Class for modification residues

ModificationSite dataclass

ModificationSite(*, id_: str = make_uuid4_as_str(), name: str | None = None, active: bool = False)

Bases: Region

Class for modification sites

ModificationState

Bases: Enum

Class for modification states

Modulation dataclass

Modulation(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: KnownOrUnknownModulation

Class for modulations

ModulationLayout dataclass

ModulationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 8.0, arrowhead_width: float = 15.0)

Bases: CellDesignerSingleHeadedArc

Class for modulation layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

Modulator dataclass

Modulator(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)

Bases: KnownOrUnknownModulator

Class for modulators

NegativeInfluence dataclass

NegativeInfluence(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: Modulation

Class for negative influences

NotGate dataclass

NotGate(*, id_: str = make_uuid4_as_str(), inputs: frozenset[Species] = frozenset())

Bases: BooleanLogicGate

Class for not gates

NotGateLayout dataclass

NotGateLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 15.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 15.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: _SimpleNodeMixin, _TextMixin, CellDesignerNode

Class for not gate layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

OrGate dataclass

OrGate(*, id_: str = make_uuid4_as_str(), inputs: frozenset[Species] = frozenset())

Bases: BooleanLogicGate

Class for or gates

OrGateLayout dataclass

OrGateLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 15.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 15.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: _SimpleNodeMixin, _TextMixin, CellDesignerNode

Class for or gate layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

OvalCompartmentLayout dataclass

OvalCompartmentLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 16.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 16.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, inner_fill: NoneValueType | Color | None = white, inner_stroke: NoneValueType | Color | None = black, inner_stroke_width: float | None = 1.0, sep: float = 12.0)

Bases: _SimpleNodeMixin, CellDesignerNode

Class for oval compartment layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Phenotype dataclass

Phenotype(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1)

Bases: Species

Class for phenotypes

PhenotypeLayout dataclass

PhenotypeLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, angle: float = 60.0)

Bases: _MultiNodeMixin, CellDesignerNode

Class for phenotype layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
angle	float	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = 60.0

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/celldesigner/core.py

def east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint3()

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/celldesigner/core.py

def east_north_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint3() / 2 + shape.joint2() / 2

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/celldesigner/core.py

def east_south_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() / 2 + shape.joint3() / 2

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/celldesigner/core.py

def north(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1() / 2 + shape.joint2() / 2

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint2()

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_north_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1() * 0.25 + shape.joint2() * 0.75

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_north_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1() * 0.75 + shape.joint2() * 0.25

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1()

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/celldesigner/core.py

def south(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint5() / 2 + shape.joint4() / 2

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4()

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_south_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint5() * 0.25 + shape.joint4() * 0.75

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_south_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint5() * 0.75 + shape.joint4() * 0.25

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint5()

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/celldesigner/core.py

def west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint6()

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/celldesigner/core.py

def west_north_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint6() / 2 + shape.joint1() / 2

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/celldesigner/core.py

def west_south_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint6() / 2 + shape.joint5() / 2

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

PhysicalStimulation dataclass

PhysicalStimulation(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: Modulation

Class for physical stimulations

PhysicalStimulationLayout dataclass

PhysicalStimulationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)

Bases: CellDesignerSingleHeadedArc

Class for physical stimulation layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

PhysicalStimulator dataclass

PhysicalStimulator(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)

Bases: Modulator

Class for physical stimulators

PositiveInfluence dataclass

PositiveInfluence(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: Modulation

Class for positive influences

PositiveInfluenceLayout dataclass

PositiveInfluenceLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = NoneValue, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 2.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)

Bases: CellDesignerSingleHeadedArc

Class for positive influence layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

Product dataclass

Product(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species, stoichiometry: int | None = None, base: bool = False)

Bases: SpeciesReference, CellDesignerModelElement

Class for products

ProductionLayout dataclass

ProductionLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = black, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 8.0, arrowhead_width: float = 15.0)

Bases: CellDesignerSingleHeadedArc

Class for production layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

Protein dataclass

Protein(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: ProteinTemplate, modifications: frozenset[Modification] = frozenset(), structural_states: frozenset[StructuralState] = frozenset())

Bases: Species

Base class for proteins

ProteinBindingDomain dataclass

ProteinBindingDomain(*, id_: str = make_uuid4_as_str(), name: str | None = None, active: bool = False)

Bases: Region

Class for protein binding domains

ProteinTemplate dataclass

ProteinTemplate(*, id_: str = make_uuid4_as_str(), name: str, modification_residues: frozenset[ModificationResidue] = frozenset())

Bases: SpeciesTemplate

Base class for protein templates

RNA dataclass

RNA(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: RNATemplate, modifications: frozenset[Modification] = frozenset())

Bases: Species

Class for RNAs

RNALayout dataclass

RNALayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, angle: float = 45.0)

Bases: _MultiNodeMixin, CellDesignerNode

Class for RNA layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
angle	float	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = 45.0

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/celldesigner/core.py

def east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint3() / 2 + shape.joint2() / 2

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/celldesigner/core.py

def east_north_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint3() * 0.25 + shape.joint2() * 0.75

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/celldesigner/core.py

def east_south_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint3() * 0.75 + shape.joint2() * 0.25

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/celldesigner/core.py

def north(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1() / 2 + shape.joint2() / 2

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint2()

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_north_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1() * 0.25 + shape.joint2() * 0.75

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_north_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1() * 0.75 + shape.joint2() * 0.25

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1()

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/celldesigner/core.py

def south(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() / 2 + shape.joint3() / 2

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint3()

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_south_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() * 0.25 + shape.joint3() * 0.75

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_south_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() * 0.75 + shape.joint3() * 0.25

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4()

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/celldesigner/core.py

def west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() / 2 + shape.joint1() / 2

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/celldesigner/core.py

def west_north_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() * 0.25 + shape.joint1() * 0.75

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/celldesigner/core.py

def west_south_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() * 0.75 + shape.joint1() * 0.25

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

RNATemplate dataclass

RNATemplate(*, id_: str = make_uuid4_as_str(), name: str, regions: frozenset[ModificationSite | CodingRegion | ProteinBindingDomain] = frozenset())

Bases: SpeciesTemplate

Class for RNA templates

Reactant dataclass

Reactant(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species, stoichiometry: int | None = None, base: bool = False)

Bases: SpeciesReference, CellDesignerModelElement

Class for reactants

Reaction dataclass

Reaction(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())

Bases: Reaction, CellDesignerModelElement

Base class for reactions

Receptor dataclass

Receptor(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: ReceptorTemplate, modifications: frozenset[Modification] = frozenset(), structural_states: frozenset[StructuralState] = frozenset())

Bases: Protein

Class for receptors

ReceptorLayout dataclass

ReceptorLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, vertical_truncation: float = 0.1)

Bases: _MultiNodeMixin, CellDesignerNode

Class for receptor layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/celldesigner/core.py

def east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() / 2 + shape.joint3() / 2

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/celldesigner/core.py

def east_north_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() * 0.25 + shape.joint3() * 0.75

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/celldesigner/core.py

def east_south_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4() * 0.75 + shape.joint3() * 0.25

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/celldesigner/core.py

def north(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint2()

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint3()

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_north_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint2() * 0.25 + shape.joint3() * 0.75

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_north_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1() / 2 + shape.joint2() / 2

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/celldesigner/core.py

def north_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint1()

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/celldesigner/core.py

def south(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint5()

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint4()

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_south_east(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint5() / 2 + shape.joint4() / 2

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_south_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint6() / 2 + shape.joint5() / 2

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/celldesigner/core.py

def south_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint6()

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/celldesigner/core.py

def west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint6() / 2 + shape.joint1() / 2

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/celldesigner/core.py

def west_north_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint6() * 0.25 + shape.joint1() * 0.75

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/celldesigner/core.py

def west_south_west(self) -> momapy.geometry.Point:
    width = self.width - self.offset * (self._n - 1)
    height = self.height - self.offset * (self._n - 1)
    position = self.position + (
        self.width / 2 - width / 2,
        self.height / 2 - height / 2,
    )
    shape = self._make_subunit_shape(position, width, height)
    return shape.joint6() * 0.75 + shape.joint1() * 0.25

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

ReceptorTemplate dataclass

ReceptorTemplate(*, id_: str = make_uuid4_as_str(), name: str, modification_residues: frozenset[ModificationResidue] = frozenset())

Bases: ProteinTemplate

Class for receptor templates

RectangleCompartmentLayout dataclass

RectangleCompartmentLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 16.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 16.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, inner_fill: NoneValueType | Color | None = white, inner_rounded_corners: float = 10.0, inner_stroke: NoneValueType | Color | None = black, inner_stroke_width: float | None = 1.0, rounded_corners: float = 10.0, sep: float = 12.0)

Bases: _SimpleNodeMixin, CellDesignerNode

Class for rectangle compartment layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Region dataclass

Region(*, id_: str = make_uuid4_as_str(), name: str | None = None, active: bool = False)

Bases: CellDesignerModelElement

Class for regions

RegulatoryRegion dataclass

RegulatoryRegion(*, id_: str = make_uuid4_as_str(), name: str | None = None, active: bool = False)

Bases: Region

Class for regulatory regions

SimpleMolecule dataclass

SimpleMolecule(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1)

Bases: Species

Class for simple molecules

SimpleMoleculeLayout dataclass

SimpleMoleculeLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1)

Bases: _MultiNodeMixin, CellDesignerNode

Class for simple chemical layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Species dataclass

Species(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1)

Bases: Species, CellDesignerModelElement

Base class for species

SpeciesTemplate dataclass

SpeciesTemplate(*, id_: str = make_uuid4_as_str(), name: str)

Bases: CellDesignerModelElement

Base class for species templates

StateTransition dataclass

StateTransition(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())

Bases: Reaction

Class for state transitions

StateTransitionLayout dataclass

StateTransitionLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 8.0, end_arrowhead_width: float = 15.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)

Bases: ReactionLayout, _ReactionNodeMixin

Class for state transition layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_arrowhead_base	Return the base anchor point of the double-headed arc end arrowhead
end_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
end_arrowhead_length	Return the length of the double-headed arc end arrowhead
end_arrowhead_tip	Return the tip anchor point of the double-headed arc end arrowhead
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the double-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base	Return the base anchor point of the double-headed arc start arrowhead
start_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
start_arrowhead_drawing_elements	Return the drawing elements of the double-headed arc start arrowhead
start_arrowhead_length	Return the length of the double-headed arc start arrowhead
start_arrowhead_tip	Return the tip anchor point of the double-headed arc start arrowhead
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_arrowhead_base

end_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc end arrowhead"""
    arrowhead_length = self.end_arrowhead_length()
    if arrowhead_length == 0:
        return self.end_point()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.end_arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

end_arrowhead_bbox

end_arrowhead_bbox()

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def end_arrowhead_bbox(self):
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.end_arrowhead_drawing_elements()
    )

end_arrowhead_border

end_arrowhead_border(point)

Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def end_arrowhead_border(self, point):
    """Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.end_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.end_arrowhead_tip()
    return point

end_arrowhead_length

end_arrowhead_length() -> float

Return the length of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc end arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._end_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

end_arrowhead_tip

end_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc end arrowhead"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the double-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the double-headed arc path"""
    start_arrowhead_length = self.start_arrowhead_length()
    end_arrowhead_length = self.end_arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten + start_arrowhead_length, "start")
            .shortened(self.end_shorten + end_arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten + start_arrowhead_length, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + end_arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerDoubleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_arrowhead_base

start_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc start arrowhead"""
    arrowhead_length = self.start_arrowhead_length()
    if arrowhead_length == 0:
        return self.start_point()
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return self.start_arrowhead_tip() + (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.start_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

start_arrowhead_bbox

start_arrowhead_bbox() -> Bbox

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.start_arrowhead_drawing_elements()
    )

start_arrowhead_border

start_arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def start_arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    point = momapy.drawing.get_drawing_elements_border(
        self.start_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.start_arrowhead_tip()
    return point

start_arrowhead_drawing_elements

start_arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the double-headed arc start arrowhead"""
    drawing_elements = self._start_arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_start_arrowhead",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_start_arrowhead",
        fill=self.start_arrowhead_fill,
        filter=self.start_arrowhead_filter,
        stroke=self.start_arrowhead_stroke,
        stroke_dasharray=self.start_arrowhead_stroke_dasharray,
        stroke_dashoffset=self.start_arrowhead_stroke_dashoffset,
        stroke_width=self.start_arrowhead_stroke_width,
        transform=self.start_arrowhead_transform,
    )
    transformation = self._get_start_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

start_arrowhead_length

start_arrowhead_length() -> float

Return the length of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc start arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._start_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return abs(bbox.west().x)

start_arrowhead_tip

start_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc start arrowhead"""
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.start_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

StructuralState dataclass

StructuralState(*, id_: str = make_uuid4_as_str(), value: str | None = None)

Bases: CellDesignerModelElement

Class for structural states

StructuralStateLayout dataclass

StructuralStateLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 16.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 50.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: _SimpleNodeMixin, CellDesignerNode

Class for structural states layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Transcription dataclass

Transcription(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())

Bases: Reaction

Class for transcriptions

TranscriptionLayout dataclass

TranscriptionLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4, 2, 4, 2, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 8.0, end_arrowhead_width: float = 15.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)

Bases: ReactionLayout, _ReactionNodeMixin

Class for transcription layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_arrowhead_base	Return the base anchor point of the double-headed arc end arrowhead
end_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
end_arrowhead_length	Return the length of the double-headed arc end arrowhead
end_arrowhead_tip	Return the tip anchor point of the double-headed arc end arrowhead
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the double-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base	Return the base anchor point of the double-headed arc start arrowhead
start_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
start_arrowhead_drawing_elements	Return the drawing elements of the double-headed arc start arrowhead
start_arrowhead_length	Return the length of the double-headed arc start arrowhead
start_arrowhead_tip	Return the tip anchor point of the double-headed arc start arrowhead
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_arrowhead_base

end_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc end arrowhead"""
    arrowhead_length = self.end_arrowhead_length()
    if arrowhead_length == 0:
        return self.end_point()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.end_arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

end_arrowhead_bbox

end_arrowhead_bbox()

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def end_arrowhead_bbox(self):
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.end_arrowhead_drawing_elements()
    )

end_arrowhead_border

end_arrowhead_border(point)

Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def end_arrowhead_border(self, point):
    """Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.end_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.end_arrowhead_tip()
    return point

end_arrowhead_length

end_arrowhead_length() -> float

Return the length of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc end arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._end_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

end_arrowhead_tip

end_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc end arrowhead"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the double-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the double-headed arc path"""
    start_arrowhead_length = self.start_arrowhead_length()
    end_arrowhead_length = self.end_arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten + start_arrowhead_length, "start")
            .shortened(self.end_shorten + end_arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten + start_arrowhead_length, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + end_arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerDoubleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_arrowhead_base

start_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc start arrowhead"""
    arrowhead_length = self.start_arrowhead_length()
    if arrowhead_length == 0:
        return self.start_point()
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return self.start_arrowhead_tip() + (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.start_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

start_arrowhead_bbox

start_arrowhead_bbox() -> Bbox

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.start_arrowhead_drawing_elements()
    )

start_arrowhead_border

start_arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def start_arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    point = momapy.drawing.get_drawing_elements_border(
        self.start_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.start_arrowhead_tip()
    return point

start_arrowhead_drawing_elements

start_arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the double-headed arc start arrowhead"""
    drawing_elements = self._start_arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_start_arrowhead",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_start_arrowhead",
        fill=self.start_arrowhead_fill,
        filter=self.start_arrowhead_filter,
        stroke=self.start_arrowhead_stroke,
        stroke_dasharray=self.start_arrowhead_stroke_dasharray,
        stroke_dashoffset=self.start_arrowhead_stroke_dashoffset,
        stroke_width=self.start_arrowhead_stroke_width,
        transform=self.start_arrowhead_transform,
    )
    transformation = self._get_start_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

start_arrowhead_length

start_arrowhead_length() -> float

Return the length of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc start arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._start_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return abs(bbox.west().x)

start_arrowhead_tip

start_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc start arrowhead"""
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.start_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

TranscriptionStartingSiteL dataclass

TranscriptionStartingSiteL(*, id_: str = make_uuid4_as_str(), name: str | None = None, active: bool = False)

Bases: Region

Class for left transcription starting sites

TranscriptionStartingSiteR dataclass

TranscriptionStartingSiteR(*, id_: str = make_uuid4_as_str(), name: str | None = None, active: bool = False)

Bases: Region

Class for right transcription starting sites

Translation dataclass

Translation(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())

Bases: Reaction

Class for translation

TranslationLayout dataclass

TranslationLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4, 2, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 8.0, end_arrowhead_width: float = 15.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)

Bases: ReactionLayout, _ReactionNodeMixin

Class for translation layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_arrowhead_base	Return the base anchor point of the double-headed arc end arrowhead
end_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
end_arrowhead_length	Return the length of the double-headed arc end arrowhead
end_arrowhead_tip	Return the tip anchor point of the double-headed arc end arrowhead
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the double-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base	Return the base anchor point of the double-headed arc start arrowhead
start_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
start_arrowhead_drawing_elements	Return the drawing elements of the double-headed arc start arrowhead
start_arrowhead_length	Return the length of the double-headed arc start arrowhead
start_arrowhead_tip	Return the tip anchor point of the double-headed arc start arrowhead
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_arrowhead_base

end_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc end arrowhead"""
    arrowhead_length = self.end_arrowhead_length()
    if arrowhead_length == 0:
        return self.end_point()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.end_arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

end_arrowhead_bbox

end_arrowhead_bbox()

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def end_arrowhead_bbox(self):
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.end_arrowhead_drawing_elements()
    )

end_arrowhead_border

end_arrowhead_border(point)

Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def end_arrowhead_border(self, point):
    """Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.end_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.end_arrowhead_tip()
    return point

end_arrowhead_length

end_arrowhead_length() -> float

Return the length of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc end arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._end_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

end_arrowhead_tip

end_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc end arrowhead"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the double-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the double-headed arc path"""
    start_arrowhead_length = self.start_arrowhead_length()
    end_arrowhead_length = self.end_arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten + start_arrowhead_length, "start")
            .shortened(self.end_shorten + end_arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten + start_arrowhead_length, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + end_arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerDoubleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_arrowhead_base

start_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc start arrowhead"""
    arrowhead_length = self.start_arrowhead_length()
    if arrowhead_length == 0:
        return self.start_point()
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return self.start_arrowhead_tip() + (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.start_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

start_arrowhead_bbox

start_arrowhead_bbox() -> Bbox

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.start_arrowhead_drawing_elements()
    )

start_arrowhead_border

start_arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def start_arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    point = momapy.drawing.get_drawing_elements_border(
        self.start_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.start_arrowhead_tip()
    return point

start_arrowhead_drawing_elements

start_arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the double-headed arc start arrowhead"""
    drawing_elements = self._start_arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_start_arrowhead",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_start_arrowhead",
        fill=self.start_arrowhead_fill,
        filter=self.start_arrowhead_filter,
        stroke=self.start_arrowhead_stroke,
        stroke_dasharray=self.start_arrowhead_stroke_dasharray,
        stroke_dashoffset=self.start_arrowhead_stroke_dashoffset,
        stroke_width=self.start_arrowhead_stroke_width,
        transform=self.start_arrowhead_transform,
    )
    transformation = self._get_start_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

start_arrowhead_length

start_arrowhead_length() -> float

Return the length of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc start arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._start_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return abs(bbox.west().x)

start_arrowhead_tip

start_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc start arrowhead"""
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.start_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

Transport dataclass

Transport(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())

Bases: Reaction

Class for transports

TransportLayout dataclass

TransportLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_bar_height: float = 8.0, end_arrowhead_sep: float = 5.0, end_arrowhead_triangle_height: float = 8.0, end_arrowhead_triangle_width: float = 15.0, start_arrowhead_bar_height: float = 8.0, start_arrowhead_sep: float = 4.0, start_arrowhead_triangle_height: float = 8.0, start_arrowhead_triangle_width: float = 15.0)

Bases: ReactionLayout, _ReactionNodeMixin

Class for transport layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_arrowhead_base	Return the base anchor point of the double-headed arc end arrowhead
end_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
end_arrowhead_length	Return the length of the double-headed arc end arrowhead
end_arrowhead_tip	Return the tip anchor point of the double-headed arc end arrowhead
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the double-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base	Return the base anchor point of the double-headed arc start arrowhead
start_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
start_arrowhead_drawing_elements	Return the drawing elements of the double-headed arc start arrowhead
start_arrowhead_length	Return the length of the double-headed arc start arrowhead
start_arrowhead_tip	Return the tip anchor point of the double-headed arc start arrowhead
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_arrowhead_base

end_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc end arrowhead"""
    arrowhead_length = self.end_arrowhead_length()
    if arrowhead_length == 0:
        return self.end_point()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.end_arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

end_arrowhead_bbox

end_arrowhead_bbox()

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def end_arrowhead_bbox(self):
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.end_arrowhead_drawing_elements()
    )

end_arrowhead_border

end_arrowhead_border(point)

Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def end_arrowhead_border(self, point):
    """Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.end_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.end_arrowhead_tip()
    return point

end_arrowhead_length

end_arrowhead_length() -> float

Return the length of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc end arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._end_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

end_arrowhead_tip

end_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc end arrowhead"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the double-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the double-headed arc path"""
    start_arrowhead_length = self.start_arrowhead_length()
    end_arrowhead_length = self.end_arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten + start_arrowhead_length, "start")
            .shortened(self.end_shorten + end_arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten + start_arrowhead_length, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + end_arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerDoubleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_arrowhead_base

start_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc start arrowhead"""
    arrowhead_length = self.start_arrowhead_length()
    if arrowhead_length == 0:
        return self.start_point()
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return self.start_arrowhead_tip() + (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.start_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

start_arrowhead_bbox

start_arrowhead_bbox() -> Bbox

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.start_arrowhead_drawing_elements()
    )

start_arrowhead_border

start_arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def start_arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    point = momapy.drawing.get_drawing_elements_border(
        self.start_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.start_arrowhead_tip()
    return point

start_arrowhead_drawing_elements

start_arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the double-headed arc start arrowhead"""
    drawing_elements = self._start_arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_start_arrowhead",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_start_arrowhead",
        fill=self.start_arrowhead_fill,
        filter=self.start_arrowhead_filter,
        stroke=self.start_arrowhead_stroke,
        stroke_dasharray=self.start_arrowhead_stroke_dasharray,
        stroke_dashoffset=self.start_arrowhead_stroke_dashoffset,
        stroke_width=self.start_arrowhead_stroke_width,
        transform=self.start_arrowhead_transform,
    )
    transformation = self._get_start_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

start_arrowhead_length

start_arrowhead_length() -> float

Return the length of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc start arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._start_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return abs(bbox.west().x)

start_arrowhead_tip

start_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc start arrowhead"""
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.start_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

Trigger dataclass

Trigger(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)

Bases: Modulator

Class for triggers

Triggering dataclass

Triggering(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: Modulation

Class for triggerings

TriggeringLayout dataclass

TriggeringLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_bar_height: float = 8.0, arrowhead_sep: float = 5.0, arrowhead_triangle_height: float = 10.0, arrowhead_triangle_width: float = 15.0)

Bases: CellDesignerSingleHeadedArc

Class for triggering layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

TruncatedProtein dataclass

TruncatedProtein(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: TruncatedProteinTemplate, modifications: frozenset[Modification] = frozenset(), structural_states: frozenset[StructuralState] = frozenset())

Bases: Protein

Class for truncated proteins

TruncatedProteinLayout dataclass

TruncatedProteinLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, rounded_corners: float = 15.0, vertical_truncation: float = 0.4, horizontal_truncation: float = 0.2)

Bases: _MultiNodeMixin, CellDesignerNode

Class for truncated protein layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

TruncatedProteinTemplate dataclass

TruncatedProteinTemplate(*, id_: str = make_uuid4_as_str(), name: str, modification_residues: frozenset[ModificationResidue] = frozenset())

Bases: ProteinTemplate

Class for truncated protein templates

Truncation dataclass

Truncation(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())

Bases: Reaction

Class for truncations

TruncationLayout dataclass

TruncationLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = white, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 10.0, end_arrowhead_sep: float = 2.0, end_arrowhead_width: float = 10.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)

Bases: ReactionLayout, _ReactionNodeMixin

Class for truncation layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_arrowhead_base	Return the base anchor point of the double-headed arc end arrowhead
end_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
end_arrowhead_length	Return the length of the double-headed arc end arrowhead
end_arrowhead_tip	Return the tip anchor point of the double-headed arc end arrowhead
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the double-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base	Return the base anchor point of the double-headed arc start arrowhead
start_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
start_arrowhead_drawing_elements	Return the drawing elements of the double-headed arc start arrowhead
start_arrowhead_length	Return the length of the double-headed arc start arrowhead
start_arrowhead_tip	Return the tip anchor point of the double-headed arc start arrowhead
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_arrowhead_base

end_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc end arrowhead"""
    arrowhead_length = self.end_arrowhead_length()
    if arrowhead_length == 0:
        return self.end_point()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.end_arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

end_arrowhead_bbox

end_arrowhead_bbox()

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def end_arrowhead_bbox(self):
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.end_arrowhead_drawing_elements()
    )

end_arrowhead_border

end_arrowhead_border(point)

Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def end_arrowhead_border(self, point):
    """Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.end_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.end_arrowhead_tip()
    return point

end_arrowhead_length

end_arrowhead_length() -> float

Return the length of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc end arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._end_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

end_arrowhead_tip

end_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc end arrowhead"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the double-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the double-headed arc path"""
    start_arrowhead_length = self.start_arrowhead_length()
    end_arrowhead_length = self.end_arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten + start_arrowhead_length, "start")
            .shortened(self.end_shorten + end_arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten + start_arrowhead_length, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + end_arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerDoubleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_arrowhead_base

start_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc start arrowhead"""
    arrowhead_length = self.start_arrowhead_length()
    if arrowhead_length == 0:
        return self.start_point()
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return self.start_arrowhead_tip() + (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.start_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

start_arrowhead_bbox

start_arrowhead_bbox() -> Bbox

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.start_arrowhead_drawing_elements()
    )

start_arrowhead_border

start_arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def start_arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    point = momapy.drawing.get_drawing_elements_border(
        self.start_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.start_arrowhead_tip()
    return point

start_arrowhead_drawing_elements

start_arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the double-headed arc start arrowhead"""
    drawing_elements = self._start_arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_start_arrowhead",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_start_arrowhead",
        fill=self.start_arrowhead_fill,
        filter=self.start_arrowhead_filter,
        stroke=self.start_arrowhead_stroke,
        stroke_dasharray=self.start_arrowhead_stroke_dasharray,
        stroke_dashoffset=self.start_arrowhead_stroke_dashoffset,
        stroke_width=self.start_arrowhead_stroke_width,
        transform=self.start_arrowhead_transform,
    )
    transformation = self._get_start_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

start_arrowhead_length

start_arrowhead_length() -> float

Return the length of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc start arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._start_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return abs(bbox.west().x)

start_arrowhead_tip

start_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc start arrowhead"""
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.start_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

Unknown dataclass

Unknown(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1)

Bases: Species

Class for unknown species

UnknownCatalysis dataclass

UnknownCatalysis(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: UnknownModulation

Class for unknown catalyses

UnknownCatalysisLayout dataclass

UnknownCatalysisLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 7.0, arrowhead_width: float = 7.0)

Bases: CellDesignerSingleHeadedArc

Class for unknown catalysis layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

UnknownCatalyzer dataclass

UnknownCatalyzer(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)

Bases: UnknownModulator

Class for unknown catalyzers

UnknownGate dataclass

UnknownGate(*, id_: str = make_uuid4_as_str(), inputs: frozenset[Species] = frozenset())

Bases: BooleanLogicGate

Class for unknown gates

UnknownGateLayout dataclass

UnknownGateLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 15.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 15.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: _SimpleNodeMixin, _TextMixin, CellDesignerNode

Class for unknown gate layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

UnknownInhibition dataclass

UnknownInhibition(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: UnknownModulation

Class for unknown inhibitions

UnknownInhibitionLayout dataclass

UnknownInhibitionLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 3.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = None, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0)

Bases: CellDesignerSingleHeadedArc

Class for unknown inhibition layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

UnknownInhibitor dataclass

UnknownInhibitor(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)

Bases: UnknownModulator

Class for unknown inhibitors

UnknownLayout dataclass

UnknownLayout(stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, fill: NoneValueType | Color | None = gray, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = NoneValue, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1)

Bases: _MultiNodeMixin, CellDesignerNode

Class for unknown species layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

UnknownModulation dataclass

UnknownModulation(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: KnownOrUnknownModulation

Class for unknown modulations

UnknownModulationLayout dataclass

UnknownModulationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 8.0, arrowhead_width: float = 15.0)

Bases: CellDesignerSingleHeadedArc

Class for unknown modulation layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

UnknownModulator dataclass

UnknownModulator(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)

Bases: KnownOrUnknownModulator

Class for unknown modulators

UnknownNegativeInfluence dataclass

UnknownNegativeInfluence(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: UnknownModulation

Class for unknown negative influences

UnknownPhysicalStimulation dataclass

UnknownPhysicalStimulation(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: UnknownModulation

Class for unknown physical stimulations

UnknownPhysicalStimulationLayout dataclass

UnknownPhysicalStimulationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)

Bases: CellDesignerSingleHeadedArc

Class for unknown physical stimulation layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

UnknownPositiveInfluence dataclass

UnknownPositiveInfluence(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: UnknownModulation

Class for unknown positive influences

UnknownPositiveInfluenceLayout dataclass

UnknownPositiveInfluenceLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = NoneValue, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 2.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)

Bases: CellDesignerSingleHeadedArc

Class for unknown positive influence layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

UnknownTransition dataclass

UnknownTransition(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())

Bases: Reaction

Class for unknown transitions

UnknownTransitionLayout dataclass

UnknownTransitionLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 8.0, end_arrowhead_width: float = 15.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)

Bases: ReactionLayout, _ReactionNodeMixin

Class for unknown transition layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_arrowhead_base	Return the base anchor point of the double-headed arc end arrowhead
end_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
end_arrowhead_length	Return the length of the double-headed arc end arrowhead
end_arrowhead_tip	Return the tip anchor point of the double-headed arc end arrowhead
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the double-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base	Return the base anchor point of the double-headed arc start arrowhead
start_arrowhead_bbox	Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border	Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
start_arrowhead_drawing_elements	Return the drawing elements of the double-headed arc start arrowhead
start_arrowhead_length	Return the length of the double-headed arc start arrowhead
start_arrowhead_tip	Return the tip anchor point of the double-headed arc start arrowhead
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_arrowhead_base

end_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc end arrowhead"""
    arrowhead_length = self.end_arrowhead_length()
    if arrowhead_length == 0:
        return self.end_point()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.end_arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

end_arrowhead_bbox

end_arrowhead_bbox()

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def end_arrowhead_bbox(self):
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.end_arrowhead_drawing_elements()
    )

end_arrowhead_border

end_arrowhead_border(point)

Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def end_arrowhead_border(self, point):
    """Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.end_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.end_arrowhead_tip()
    return point

end_arrowhead_length

end_arrowhead_length() -> float

Return the length of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc end arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._end_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

end_arrowhead_tip

end_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc end arrowhead"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the double-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the double-headed arc path"""
    start_arrowhead_length = self.start_arrowhead_length()
    end_arrowhead_length = self.end_arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten + start_arrowhead_length, "start")
            .shortened(self.end_shorten + end_arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten + start_arrowhead_length, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + end_arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerDoubleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_arrowhead_base

start_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc start arrowhead"""
    arrowhead_length = self.start_arrowhead_length()
    if arrowhead_length == 0:
        return self.start_point()
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return self.start_arrowhead_tip() + (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.start_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

start_arrowhead_bbox

start_arrowhead_bbox() -> Bbox

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.start_arrowhead_drawing_elements()
    )

start_arrowhead_border

start_arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def start_arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    point = momapy.drawing.get_drawing_elements_border(
        self.start_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.start_arrowhead_tip()
    return point

start_arrowhead_drawing_elements

start_arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the double-headed arc start arrowhead"""
    drawing_elements = self._start_arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_start_arrowhead",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_start_arrowhead",
        fill=self.start_arrowhead_fill,
        filter=self.start_arrowhead_filter,
        stroke=self.start_arrowhead_stroke,
        stroke_dasharray=self.start_arrowhead_stroke_dasharray,
        stroke_dashoffset=self.start_arrowhead_stroke_dashoffset,
        stroke_width=self.start_arrowhead_stroke_width,
        transform=self.start_arrowhead_transform,
    )
    transformation = self._get_start_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

start_arrowhead_length

start_arrowhead_length() -> float

Return the length of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc start arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._start_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return abs(bbox.west().x)

start_arrowhead_tip

start_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc start arrowhead"""
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.start_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

UnknownTriggering dataclass

UnknownTriggering(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)

Bases: UnknownModulation

Class for unknown triggerings

UnknownTriggeringLayout dataclass

UnknownTriggeringLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_bar_height: float = 8.0, arrowhead_sep: float = 5.0, arrowhead_triangle_height: float = 10.0, arrowhead_triangle_width: float = 15.0)

Bases: CellDesignerSingleHeadedArc

Class for unknown triggering layouts

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the group layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name: str) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = momapy.geometry.Bbox(
        momapy.geometry.Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements()

Return the self drawing elements of the single-headed arc

Source code in src/momapy/celldesigner/core.py

def self_drawing_elements(self):
    drawing_elements = momapy.builder.super_or_builder(
        CellDesignerSingleHeadedArc, self
    ).self_drawing_elements()
    done_bases = []
    for base in type(self).__mro__:
        if (
            momapy.builder.issubclass_or_builder(base, momapy.sbgn.core._SBGNMixin)
            and base is not type(self)
            and not any([issubclass(done_base, base) for done_base in done_bases])
        ):
            drawing_elements += getattr(base, "_mixin_drawing_elements")(self)
            done_bases.append(base)
    return drawing_elements

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)